Move include statements out of workflow definition

main.nf

@@ -104,49 +104,49 @@ def run_info_message() {
  log.info "========================================="
 }
 
+include {align_reads} from './workflows/align_wf'
+include {count_features} from './workflows/featureCounts_wf'
+include {quant_exons} from './workflows/exonQuant_wf'
+include {quant_tx} from './workflows/txQuant_wf'
+include {quant_txrev} from './workflows/txrevQuant_wf'
+include {quant_leafcutter} from './workflows/leafcutter_wf'
+include { createBigWig } from './modules/utils'
+include { generate_mbv } from './workflows/mbv_wf'
+include { sample_correlation } from './modules/utils'
+
 workflow {
  run_info_message()
-
- include {align_reads} from './workflows/align_wf'
  align_reads()
 
  if (params.run_ge_quant){
- include {count_features} from './workflows/featureCounts_wf'
  count_features(align_reads.out.bam_sorted_by_name)
  }
 
  if (params.run_exon_quant) {
- include {quant_exons} from './workflows/exonQuant_wf'
  quant_exons(align_reads.out.bam_sorted_by_name)
  }
 
  if (params.run_salmon) {
- include {quant_tx} from './workflows/txQuant_wf'
  quant_tx(align_reads.out.trimmed_reads)
  }
 
  if (params.run_txrevise) {
- include {quant_txrev} from './workflows/txrevQuant_wf'
  quant_txrev(align_reads.out.trimmed_reads)
  }
 
  if (params.run_leafcutter) {
- include {quant_leafcutter} from './workflows/leafcutter_wf'
  quant_leafcutter(align_reads.out.bam_sorted_indexed)
  }
 
  if (params.generate_bigwig) {
- include { createBigWig } from './modules/utils'
  createBigWig(align_reads.out.bam_sorted_indexed)
  }
 
  if (params.run_mbv){
- include { generate_mbv } from './workflows/mbv_wf'
  generate_mbv(align_reads.out.bam_sorted_indexed)
  }
 
  if (params.run_sample_corr && params.run_ge_quant) { 
- include { sample_correlation } from './modules/utils'
  sample_correlation(count_features.out.gene_feature_counts.collect(),
  Channel.fromPath("$baseDir/assets/mdsplot_header.txt"),
  Channel.fromPath("$baseDir/assets/heatmap_header.txt"))